I have noticed similiar thing. One of my sites had wrong backlinks for many years - they were href="http://domain.sth" instead of href="http://domain.sth/". The backlinks have been corrected some months ago, but the Pagerank hasn't been reindexed for them so far.

All PR checking tools show 0 for query "http://domain.sth/" while PR 2 for "http://domain.sth". Some days ago I noticed, that query "http://domain.sth/index.html" returns PR 2 too, while correct URL "http://domain.sth/" shows 0. And none of these urls is indexed. I think this lack of indexing might be a penalty, but I'm not sure about it. The weird PR behaviour is clearly because of having wrong backlinks in past.

I also have the same thing, the main page has grayed out PR while the inner pages do have PR. I thought that was sth specific to my site because I recently changed my web site address from my computer at school (myschool.edu/#*$!/yyy/) to a new domain I purchased (domain.com). I am currently redirecting the old address to the new one. After reading this thread, I think the situation is because of a common update. However, the problem is that my previous address is removed from Google SERPs except couple pages, while my new address has much much much lower positions in the Google SERPs. I hope this'll change soon. On MSN, on the contrary, my new address has a better position than the old one (mid 1st page vs mid 2nd page on the main search term) since I searched through the web and got 10-20 inbound links after getting my new domain. My traffic was mainly from google though, and I have a little less than half the visitors compared to previous couple days now.

Thanks for the replies. I tried to clean the cache and to refresh, they didn't work but when I found another computer to try, it showed the page rank as it was before. My web site is not a source of real revenue but I feel relieved anyway :) There is still a problem with the low SERP listings but I hope that is related to the domain name change I performed. I did the 301 redirect from the old address as well, so it should get ok in the next Google update.